相关论文: The genetic code multiplet structure, in one numbe…
In this paper we describe a class of codes called {\it permutation codes}. This class of codes is a generalization of cyclic codes and quasi-cyclic codes. We also give some examples of optimal permutation codes over binary, ternary, and…
We define a map between the set of permutations that avoid either the four patterns $3214,3241,4213,4231$ or $3124,3142,4123,4132$, and the set of Dyck prefixes. This map, when restricted to either of the two classes, turns out to be a…
It is known that all degenerations of the complex projective plane into a surface with only quotient singularities are controlled by the positive integer solutions $(a,b,c)$ of the Markov equation $$x^2+y^2+z^2=3xyz.$$ It turns out that…
We propose a partitioning of the set of unlabelled, connected cubic graphs into two disjoint subsets named genes and descendants, where the cardinality of the descendants is much larger than that of the genes. The key distinction between…
The article is devoted to phenomena of symmetries and algebras in matrix presentations of the genetic code. The Kronecker family of the genetic matrices is investigated, which is based on the alphabetical matrix [C A; U G], where C, A, U, G…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
In recent years, the emergence of DNA storage systems has led to a widespread focus on the research of codes correcting insertions, deletions, and classic substitutions. During the initial investigation, Levenshtein discovered the VT codes…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
We prove that it is decidable if a finitely based permutation class contains infinitely many simple permutations, and establish an unavoidable substructure result for simple permutations: every sufficiently long simple permutation contains…
It is a well-known fact that genetic sequences may contain sections with repeated units, called repeats, that differ in length over a population, with a length distribution of geometric type. A simple class of recombination models with…
We construct a direct natural bijection between descending plane partitions without any special part and permutations. The directness is in the sense that the bijection avoids any reference to nonintersecting lattice paths. The advantage of…
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set are of equal length. Finding an exact match for a pattern…
In this paper, we construct new families of convolutional codes. Such codes are obtained by means of algebraic geometry codes. Additionally, more families of convolutional codes are constructed by means of puncturing, extending, expanding…
In combinatorics, a derangement is a permutation of the elements of a set, such that no element appears in its original position. The number of derangement of an n-element set is called the nth derangement number. Recently, the degenerate…
A bijection between $(31245,32145,31254,32154)$-avoiding permutations and $(31425,32415,31524,32514)$-avoiding permutations is constructed, which preserves five classical set-valued statistics. Combining with two codings of permutations due…
The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code…
We characterise and enumerate permutations that are sortable by n-4 passes through a stack. We conjecture the number of permutations sortable by n-5 passes, and also the form of a formula for the general case n-k, which involves a…
We investigate permutations in terms of their cycle structure and descent set. To do this, we generalize the classical bijection of Gessel and Reutenauer to deal with permutations that have some ascending and some descending blocks. We then…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…